Updates

1 Data: primer_aufbereitet_20240917.xlsx

Primertest data

1.1 Target genes

 

1.2 IG / TR Rearrangement clases

 

1.3 CT values

1.3.1 Sample CT

toDO-1: Sample CTs <15 or >50 and those with no numeric values skipped for now.
Please correct these values in primer_aufbereitet_20240917.xlsx.
(columns: SignalCT_01, SignalCT_02, SignalCT_03, SignalCT_04)

1.3.2 BC CT

toDO-2: BC CTs <20 or >50 and those with no numeric values skipped for now.
Please correct these values in primer_aufbereitet_20240917.xlsx.
(columns: BC_01, BC_02, BC_03, BC_04)

1.4 Primer counts

Rclass 59 61 62 63 64 66 Row_Sum
VdJd 0 1 95 8 103 4 211
intronKDE 0 0 110 9 108 6 233
VdJa 0 2 142 9 149 3 305
DdJd 0 3 542 9 556 1 1111
DdJa 0 1 581 4 599 0 1185
DdDd 0 2 571 22 599 8 1202
VdDd 0 7 653 38 668 15 1381
VkKDE 0 3 689 34 706 16 1448
DbJb 0 5 736 53 779 29 1602
VkJk 0 2 837 38 877 5 1759
VbJb 0 3 1094 62 1141 35 2335
DhJh 0 8 2152 142 2168 54 4524
VgJg 0 9 3156 104 3289 1 6559
VhJh 2 12 3907 112 3584 43 7660
Column_Sum 2 58 15265 644 15326 220 31515

1.5 Signal/noise difference

1.5.1 ΔCT ~ Rclass

1.5.2 ΔCT ~ annealing temperature

1.5.3 ΔCT ~ t. gene + ann. temp.

1.5.4 ΔCT 64°C - 62°C

1.5.4.1 barplot

1.5.4.2 Scatter plot

1.5.5 ΔRN

 

1.6 Primer acceptance

1.6.1 By rearrangement class

1.6.1.1 Absolute numbers

1.6.1.2 Percentages

1.6.2 By annealing temperature

1.6.2.1 Absolute numbers

1.6.2.2 Percentages

 

2 Data: RQ_gesamt_20240917.xlsx

Follow-up data

2.1 Assay characteristics~Rclass

Only assays with an available Rclass are included. In cases with multiple time-points, only the most recent value for each assay was retained.

2.1.1 Lebens BC

toDO-3: BC CTs <20 or >50 and those with no numeric values skipped for now.
Please correct these values in the RQ_gesamt_20240917.xlsx.
(column: lebens_BC)

2.1.2 Sensitivity

2.1.3 Specifity

 

2.2 BM vs. PB MRD

BM and PB samples collected <= 7 days apart. All assays per patient and date kept.

2.2.1 B-ALL

2.2.1.1 All time-points

2.2.1.2 Samples on Blinatumomab

All datapoints from the “All time-points” plot that have “blin” in the columns visit or zeitp.

2.2.1.3 Samples after stem cell transplantation

All datapoints from the “All time-points” plot that have “sct”/“szt”/“allo”/“tx”, but not “vor” in the columns visit or zeitp.

2.2.2 T-ALL

2.2.3 MPAL

toDO-4: Distinguish B-myeloid and T-myeloid.

2.2.4 Burkitt

 

2.3 BM vs. BM-Trephine MRD

BM and BM-Trephine samples collected <= 7 days apart.

2.3.1 B-ALL

2.3.2 T-ALL

2.4 BM vs. BM-Trephine vs. PB MRD

BM, BM-Trephine and PB triplets collected <= 7 days apart.

2.4.1 B-ALL

2.4.2 T-ALL

 

2.5 Sample CT values vs. MRD

2.5.1 All rearrangement classes

Density values capped at 100 for better resolution.

toDO-5: Sample CTs <15 or >50 and those with no numeric values skipped for now.
Please correct these values in the RQ_gesamt_20240917.xlsx.
(columns: ct_1, ct_2, ct_3, MW_ct )

2.5.2 By rearrangement class

Density values capped at 50 for better resolution.

 

2.6 MRD by different target

Same dna-nr, different target.

2.6.1 IG vs TR

2.6.2 IGH vs IGK

2.6.3 IGH vs IGL

2.6.4 IGH vs TRA

2.6.5 IGH vs TRB

2.6.6 IGH vs TRG

2.6.7 IGH vs TRD

2.6.8 IGK vs IGL

2.6.9 IGK vs TRA

2.6.10 IGK vs TRB

2.6.11 IGK vs TRG

2.6.12 IGK vs TRD

2.6.13 IGL vs TRA

2.6.14 IGL vs TRB

2.6.15 IGL vs TRG

2.6.16 IGL vs TRD

2.6.17 TRA vs TRB

2.6.18 TRA vs TRG

2.6.19 TRA vs TRD

2.6.20 TRB vs TRG

2.6.21 TRB vs TRD

2.6.22 TRG vs TRD

 

2.7 Qualitative Concordance of MRD Assessments

Same dna-nr, different assays.
If more MRD values for a particular dna-nr/assay combination available, only the highest one was kept.

Click to show Shortcut explanations
Shortcut Meaning
NEG Negative
POS Positive
PBQR Positive Below Quantitative Range
UNEG Uncertain Negative

 

Click to show MRD status combinations in each concordance group